Was thinking about this when picking what color/skill combos work together. Would be great if your team could have synergy bonuses of some sort.
IE all xmen = 5% bonus damage or Mr Fantastic + Mrs Fantastic (coming eventually I hope) = 10% health bonus
There could be a ton of fun things to add this way
Could potentially be an incentive to level some other characters although in practice I doubt you could make the synergy bonuses worthwhile enough to take instead of say, using Patch.
Also, this might affect team variety negatively